Atomistry » Zinc » PDB 7lbs-7lyb » 7lps
Atomistry »
  Zinc »
    PDB 7lbs-7lyb »
      7lps »

Zinc in PDB 7lps: Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2)

Protein crystallography data

The structure of Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2), PDB code: 7lps was solved by R.P.Nowak, E.S.Fischer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 150.57 / 3.78
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 151.8, 117.292, 196.713, 90, 97.3, 90
R / Rfree (%) 28.9 / 30.3

Other elements in 7lps:

The structure of Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2) also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2) (pdb code 7lps). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2), PDB code: 7lps:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7lps

Go back to Zinc Binding Sites List in 7lps
Zinc binding site 1 out of 8 in the Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:84.8
occ:1.00
 SG B:CYS391 2.3 75.4 1.0
SG B:CYS394 2.3 99.5 1.0
SG B:CYS326 2.4 106.4 1.0
SG B:CYS323 2.6 111.5 1.0
CB B:CYS326 3.1 98.7 1.0
CB B:CYS391 3.1 77.2 1.0
CB B:CYS323 3.2 91.0 1.0
CB B:CYS394 3.5 95.1 1.0
N B:CYS394 3.8 88.0 1.0
N B:CYS326 3.9 104.1 1.0
CA B:CYS326 4.0 110.0 1.0
OG1 B:THR329 4.2 103.1 1.0
CA B:CYS394 4.2 87.1 1.0
CB B:THR329 4.3 95.9 1.0
CA B:CYS391 4.5 81.3 1.0
CG2 B:THR329 4.7 93.1 1.0
CA B:CYS323 4.7 87.2 1.0
CB B:ILE393 4.9 79.2 1.0
CB B:GLN325 4.9 100.6 1.0
C B:ILE393 4.9 92.2 1.0
C B:GLN325 4.9 100.0 1.0
N B:ILE393 5.0 80.2 1.0
C B:CYS394 5.0 92.0 1.0

Zinc binding site 2 out of 8 in 7lps

Go back to Zinc Binding Sites List in 7lps
Zinc binding site 2 out of 8 in the Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:95.7
occ:1.00
 NE2 C:HIS162 2.0 100.0 1.0
SG C:CYS142 2.3 108.0 1.0
CE1 C:HIS162 2.3 105.1 1.0
SG C:CYS145 2.4 115.4 1.0
NE2 C:HIS158 2.5 106.9 1.0
CD2 C:HIS162 3.2 102.9 1.0
CB C:CYS145 3.3 115.7 1.0
CD2 C:HIS158 3.3 92.4 1.0
CB C:CYS142 3.4 100.1 1.0
N C:CYS145 3.4 111.0 1.0
CE1 C:HIS158 3.4 118.7 1.0
ND1 C:HIS162 3.5 107.3 1.0
CA C:CYS145 3.9 108.1 1.0
CG C:HIS162 3.9 108.1 1.0
CB C:GLN144 4.1 110.9 1.0
CG C:HIS158 4.4 90.8 1.0
C C:GLN144 4.4 113.9 1.0
ND1 C:HIS158 4.5 110.4 1.0
N C:GLY146 4.6 106.3 1.0
CA C:GLN144 4.6 109.1 1.0
C C:CYS145 4.7 106.6 1.0
CA C:CYS142 4.8 95.8 1.0
N C:GLN144 4.8 107.7 1.0
CB C:ALA147 4.8 97.3 1.0
CB B:HIS397 4.9 99.6 1.0
CG C:GLN144 5.0 111.3 1.0
O C:HIS158 5.0 109.2 1.0

Zinc binding site 3 out of 8 in 7lps

Go back to Zinc Binding Sites List in 7lps
Zinc binding site 3 out of 8 in the Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1001

b:87.3
occ:1.00
 SG E:CYS394 2.2 101.4 1.0
SG E:CYS326 2.3 114.1 1.0
SG E:CYS391 2.3 86.2 1.0
SG E:CYS323 2.7 106.1 1.0
CB E:CYS326 3.1 108.3 1.0
CB E:CYS391 3.1 83.4 1.0
CB E:CYS394 3.3 101.3 1.0
CB E:CYS323 3.4 100.9 1.0
N E:CYS394 3.6 86.4 1.0
N E:CYS326 3.8 112.0 1.0
CA E:CYS326 4.0 120.9 1.0
CA E:CYS394 4.1 98.3 1.0
OG1 E:THR329 4.2 113.8 1.0
CB E:THR329 4.4 108.8 1.0
CA E:CYS391 4.6 92.6 1.0
C E:ILE393 4.8 86.7 1.0
CB E:ILE393 4.8 80.2 1.0
CB E:GLN325 4.8 116.0 1.0
C E:CYS394 4.8 98.1 1.0
CG2 E:THR329 4.9 109.1 1.0
CA E:CYS323 4.9 93.3 1.0
C E:GLN325 4.9 108.8 1.0
N E:ILE393 4.9 71.9 1.0
N E:ALA395 5.0 93.4 1.0

Zinc binding site 4 out of 8 in 7lps

Go back to Zinc Binding Sites List in 7lps
Zinc binding site 4 out of 8 in the Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:82.6
occ:1.00
 NE2 F:HIS162 2.1 82.3 1.0
SG F:CYS142 2.2 77.2 1.0
NE2 F:HIS158 2.2 117.4 1.0
SG F:CYS145 2.5 100.8 1.0
CE1 F:HIS162 2.5 86.1 1.0
CD2 F:HIS158 3.0 116.7 1.0
CB F:CYS142 3.1 94.7 1.0
CE1 F:HIS158 3.2 117.5 1.0
CD2 F:HIS162 3.3 88.6 1.0
CB F:CYS145 3.4 86.5 1.0
N F:CYS145 3.6 84.4 1.0
ND1 F:HIS162 3.7 92.0 1.0
CA F:CYS145 4.1 84.6 1.0
CG F:HIS158 4.1 117.7 1.0
CG F:HIS162 4.1 94.8 1.0
ND1 F:HIS158 4.2 121.0 1.0
CB F:GLN144 4.4 83.7 1.0
CA F:CYS142 4.6 93.5 1.0
N F:GLY146 4.6 87.5 1.0
CB F:ALA147 4.6 97.5 1.0
C F:GLN144 4.6 80.8 1.0
C F:CYS145 4.8 85.7 1.0
N F:ALA147 4.8 96.0 1.0
CA F:GLN144 4.9 80.0 1.0
O F:HIS158 4.9 114.9 1.0
N F:GLN144 4.9 92.8 1.0
C F:CYS142 5.0 92.5 1.0

Zinc binding site 5 out of 8 in 7lps

Go back to Zinc Binding Sites List in 7lps
Zinc binding site 5 out of 8 in the Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn501

b:75.4
occ:1.00
 CB H:CYS394 2.2 104.1 1.0
SG H:CYS391 2.4 84.2 1.0
SG H:CYS323 2.5 117.3 1.0
SG H:CYS326 2.8 105.8 1.0
SG H:CYS394 3.0 149.9 1.0
CB H:CYS391 3.0 86.1 1.0
CA H:CYS394 3.4 96.8 1.0
CB H:CYS326 3.5 97.1 1.0
CB H:CYS323 3.5 88.7 1.0
N H:CYS394 3.6 91.2 1.0
N H:CYS326 3.8 107.9 1.0
CA H:CYS326 4.2 104.5 1.0
CB H:GLN325 4.4 96.4 1.0
C H:CYS394 4.4 100.1 1.0
CA H:CYS391 4.5 89.0 1.0
OG H:SER396 4.6 118.6 1.0
CB H:SER396 4.6 103.1 1.0
N H:ALA395 4.6 99.2 1.0
C H:GLN325 4.7 103.8 1.0
N H:SER396 4.8 107.2 1.0
C H:ILE393 4.8 96.7 1.0
OG1 H:THR329 4.9 115.4 1.0
CA H:GLN325 5.0 97.4 1.0
CA H:CYS323 5.0 87.5 1.0

Zinc binding site 6 out of 8 in 7lps

Go back to Zinc Binding Sites List in 7lps
Zinc binding site 6 out of 8 in the Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:95.6
occ:1.00
 NE2 I:HIS162 1.9 79.6 1.0
CE1 I:HIS162 2.3 88.7 1.0
SG I:CYS142 2.4 97.7 1.0
NE2 I:HIS158 2.4 95.0 1.0
SG I:CYS145 2.5 85.1 1.0
CD2 I:HIS162 3.2 83.5 1.0
CD2 I:HIS158 3.2 85.5 1.0
CE1 I:HIS158 3.3 106.9 1.0
CB I:CYS145 3.3 99.1 1.0
CB I:CYS142 3.4 90.5 1.0
ND1 I:HIS162 3.5 95.0 1.0
N I:CYS145 3.6 86.7 1.0
CG I:HIS162 3.9 86.8 1.0
CA I:CYS145 4.0 100.2 1.0
CB I:GLN144 4.2 97.3 1.0
CG I:HIS158 4.2 98.3 1.0
ND1 I:HIS158 4.3 113.7 1.0
C I:GLN144 4.5 89.1 1.0
N I:GLY146 4.7 97.3 1.0
CA I:GLN144 4.8 99.3 1.0
CA I:CYS142 4.8 85.5 1.0
CB I:ALA147 4.8 95.0 1.0
C I:CYS145 4.8 97.1 1.0
O I:HIS158 4.9 119.3 1.0
N I:GLN144 4.9 106.5 1.0

Zinc binding site 7 out of 8 in 7lps

Go back to Zinc Binding Sites List in 7lps
Zinc binding site 7 out of 8 in the Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn1001

b:89.2
occ:1.00
 SG K:CYS394 2.2 82.1 1.0
SG K:CYS391 2.2 88.1 1.0
SG K:CYS326 2.3 94.3 1.0
SG K:CYS323 2.7 86.6 1.0
CB K:CYS326 3.1 98.0 1.0
CB K:CYS391 3.1 83.9 1.0
CB K:CYS394 3.3 87.0 1.0
CB K:CYS323 3.4 89.7 1.0
N K:CYS394 3.6 79.8 1.0
N K:CYS326 3.8 93.8 1.0
CA K:CYS326 4.0 103.0 1.0
CA K:CYS394 4.0 86.7 1.0
OG1 K:THR329 4.3 100.6 1.0
CB K:THR329 4.4 98.8 1.0
CA K:CYS391 4.6 93.6 1.0
C K:ILE393 4.7 83.3 1.0
CB K:ILE393 4.8 72.5 1.0
CB K:GLN325 4.8 105.7 1.0
C K:CYS394 4.8 83.7 1.0
CG2 K:THR329 4.8 98.5 1.0
CA K:CYS323 4.9 84.7 1.0
C K:GLN325 4.9 94.6 1.0
N K:ILE393 4.9 71.5 1.0
N K:ALA395 5.0 82.3 1.0

Zinc binding site 8 out of 8 in 7lps

Go back to Zinc Binding Sites List in 7lps
Zinc binding site 8 out of 8 in the Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn201

b:83.7
occ:1.00
 SG L:CYS145 2.2 100.0 1.0
SG L:CYS142 2.2 79.0 1.0
NE2 L:HIS162 2.3 86.5 1.0
NE2 L:HIS158 2.4 89.6 1.0
CE1 L:HIS162 2.7 88.6 1.0
CB L:CYS142 3.1 97.0 1.0
CB L:CYS145 3.1 100.3 1.0
CD2 L:HIS158 3.2 95.3 1.0
N L:CYS145 3.3 97.2 1.0
CE1 L:HIS158 3.4 91.7 1.0
CD2 L:HIS162 3.5 95.3 1.0
CA L:CYS145 3.7 98.9 1.0
ND1 L:HIS162 3.9 93.9 1.0
CB L:GLN144 4.2 105.4 1.0
N L:GLY146 4.3 98.7 1.0
CG L:HIS162 4.3 98.6 1.0
C L:GLN144 4.3 91.7 1.0
CG L:HIS158 4.3 96.4 1.0
ND1 L:HIS158 4.5 95.1 1.0
C L:CYS145 4.5 97.0 1.0
CB L:ALA147 4.5 98.9 1.0
CA L:CYS142 4.5 96.0 1.0
N L:ALA147 4.6 89.8 1.0
CA L:GLN144 4.6 99.4 1.0
N L:GLN144 4.7 103.4 1.0
CG L:GLN144 4.8 106.0 1.0
C L:CYS142 4.8 91.6 1.0
O L:CYS142 4.9 93.5 1.0

Reference:

E.S.Wang, A.L.Verano, R.P.Nowak, J.C.Yuan, K.A.Donovan, N.A.Eleuteri, H.Yue, K.H.Ngo, P.H.Lizotte, P.C.Gokhale, N.S.Gray, E.S.Fischer. Acute Pharmacological Degradation of Helios Destabilizes Regulatory T Cells Nat.Chem.Biol. 2021.
ISSN: ESSN 1552-4469
DOI: 10.1038/S41589-021-00802-W
Page generated: Tue Oct 29 22:58:52 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy